Output below are interactive Manhattan plots. The x-axis has functional terms and the y-axis has the -log10(adjust p-value). The size of the circles corresponds to the term size. Term size is the number of genes in the pathway. So, GO:1234 (5) would have a smaller circle compared to GO:5678 (100) because there are 5 genes in GO:1234 pathway vs 100 genes in the GO:5678 pathway. These plots are only showing significant results. This is why some plots cannot be generated despite 10 genes used for input into the analysis. We will use genes with an adjusted p-value < 0.05 and only usin data sources from GO:MF, GO:BP, KEGG, and TF.
runGprofiler("age","Pericytes & SMCs","up-regulated")## [1] "83 genes input into functional enrichment analysis."runGprofiler("age","Pericytes & SMCs","down-regulated")## [1] "21 genes input into functional enrichment analysis."runGprofiler("age","Vwf+Cldn5+ BECs","up-regulated")## [1] "17 genes input into functional enrichment analysis."runGprofiler("age","Vwf+Cldn5+ BECs","down-regulated")## [1] "13 genes input into functional enrichment analysis."runGprofiler("age","Vwf+ BECs & LECs","up-regulated")## [1] "50 genes input into functional enrichment analysis."runGprofiler("age","Vwf+ BECs & LECs","down-regulated")## [1] "75 genes input into functional enrichment analysis."runGprofiler("age","Kdr-high BECs & LECs","up-regulated")## [1] "86 genes input into functional enrichment analysis."runGprofiler("age","Kdr-high BECs & LECs","down-regulated")## [1] "72 genes input into functional enrichment analysis."runGprofiler("age","Doublets BECs / macrophages","up-regulated")## [1] "3 genes input into functional enrichment analysis."runGprofiler("age","Doublets BECs / macrophages","down-regulated")## [1] "2 genes input into functional enrichment analysis."runGprofiler("age","Mrc1+H2-Eb1-low macrophages","up-regulated")## [1] "215 genes input into functional enrichment analysis."runGprofiler("age","Mrc1+H2-Eb1-low macrophages","down-regulated")## [1] "159 genes input into functional enrichment analysis."runGprofiler("age","Mrc1+H2-Eb1-high macrophages","up-regulated")## [1] "84 genes input into functional enrichment analysis."runGprofiler("age","Mrc1+H2-Eb1-high macrophages","down-regulated")## [1] "37 genes input into functional enrichment analysis."runGprofiler("age","Dendritic cells","up-regulated")## [1] "387 genes input into functional enrichment analysis."runGprofiler("age","Dendritic cells","down-regulated")## [1] "70 genes input into functional enrichment analysis."runGprofiler("age","Monocytes","up-regulated")## [1] "18 genes input into functional enrichment analysis."# 3 genes input, no results to showrunGprofiler("age","Neutrophils","up-regulated")## [1] "118 genes input into functional enrichment analysis."runGprofiler("age","Neutrophils","down-regulated")## [1] "26 genes input into functional enrichment analysis."runGprofiler("age","Mast cells","up-regulated")## [1] "59 genes input into functional enrichment analysis."runGprofiler("age","Mast cells","down-regulated")## [1] "20 genes input into functional enrichment analysis."runGprofiler("age","Myeloid progenitors","up-regulated")## [1] "24 genes input into functional enrichment analysis."# 1 gene input, no results to showrunGprofiler("age","Fibroblasts","up-regulated")## [1] "114 genes input into functional enrichment analysis."runGprofiler("age","Fibroblasts","down-regulated")## [1] "82 genes input into functional enrichment analysis."runGprofiler("age","Schwann cells","up-regulated")## [1] "117 genes input into functional enrichment analysis."runGprofiler("age","Schwann cells","down-regulated")## [1] "16 genes input into functional enrichment analysis."runGprofiler("age","T cells & ILCs","up-regulated")## [1] "100 genes input into functional enrichment analysis."# 3 genes used for analysis
# only has significant results in the MIRNA sourcerunGprofiler("age","Developing B cells","up-regulated")## [1] "257 genes input into functional enrichment analysis."runGprofiler("age","Developing B cells","down-regulated")## [1] "25 genes input into functional enrichment analysis."runGprofiler("age","Mature B cells","up-regulated")## [1] "261 genes input into functional enrichment analysis."runGprofiler("age","Mature B cells","down-regulated")## [1] "100 genes input into functional enrichment analysis."# 4 genes input, no results to show# 0 genes input, no results to show# 1 gene input, no results to showrunGprofiler("isoform","Vwf+Cldn5+ BECs","down-regulated")## [1] "17 genes input into functional enrichment analysis."runGprofiler("isoform","Vwf+ BECs & LECs","up-regulated")## [1] "28 genes input into functional enrichment analysis."runGprofiler("isoform","Vwf+ BECs & LECs","down-regulated")## [1] "15 genes input into functional enrichment analysis."runGprofiler("isoform","Kdr-high BECs & LECs","up-regulated")## [1] "17 genes input into functional enrichment analysis."runGprofiler("isoform","Kdr-high BECs & LECs","down-regulated")## [1] "22 genes input into functional enrichment analysis."# 0 genes input, no results to show# 1 gene input, no results to showrunGprofiler("isoform","Mrc1+H2-Eb1-low macrophages","up-regulated")## [1] "202 genes input into functional enrichment analysis."runGprofiler("isoform","Mrc1+H2-Eb1-low macrophages","down-regulated")## [1] "82 genes input into functional enrichment analysis."runGprofiler("isoform","Mrc1+H2-Eb1-high macrophages","up-regulated")## [1] "34 genes input into functional enrichment analysis."runGprofiler("isoform","Mrc1+H2-Eb1-high macrophages","down-regulated")## [1] "18 genes input into functional enrichment analysis."runGprofiler("isoform","Dendritic cells","up-regulated")## [1] "28 genes input into functional enrichment analysis."# 9 genes input, no results to showrunGprofiler("isoform","Monocytes","up-regulated")## [1] "3 genes input into functional enrichment analysis."# 3 genes input, no results to showrunGprofiler("isoform","Neutrophils","up-regulated")## [1] "3 genes input into functional enrichment analysis."runGprofiler("isoform","Neutrophils","down-regulated")## [1] "6 genes input into functional enrichment analysis."# 3 genes input, no results to show# no genes input, no results to showrunGprofiler("isoform","Myeloid progenitors","up-regulated")## [1] "45 genes input into functional enrichment analysis."# 2 genes input, no results to showrunGprofiler("isoform","Fibroblasts","up-regulated")## [1] "14 genes input into functional enrichment analysis."runGprofiler("isoform","Fibroblasts","down-regulated")## [1] "24 genes input into functional enrichment analysis."runGprofiler("isoform","Schwann cells","up-regulated")## [1] "104 genes input into functional enrichment analysis."runGprofiler("isoform","Schwann cells","down-regulated")## [1] "26 genes input into functional enrichment analysis."runGprofiler("isoform","T cells & ILCs","up-regulated")## [1] "32 genes input into functional enrichment analysis."# 3 genes used for analysis
# only has significant results in the MIRNA sourcerunGprofiler("isoform","Developing B cells","up-regulated")## [1] "31 genes input into functional enrichment analysis."# 4 genes input, no results to showrunGprofiler("isoform","Mature B cells","up-regulated")## [1] "96 genes input into functional enrichment analysis."runGprofiler("isoform","Mature B cells","down-regulated")## [1] "9 genes input into functional enrichment analysis."# 3 genes input, no results to showrunGprofiler("sex","Pericytes & SMCs","down-regulated")## [1] "7 genes input into functional enrichment analysis."runGprofiler("sex","Vwf+Cldn5+ BECs","up-regulated")## [1] "18 genes input into functional enrichment analysis."runGprofiler("sex","Vwf+Cldn5+ BECs","down-regulated")## [1] "7 genes input into functional enrichment analysis."runGprofiler("sex","Vwf+ BECs & LECs","up-regulated")## [1] "51 genes input into functional enrichment analysis."runGprofiler("sex","Vwf+ BECs & LECs","down-regulated")## [1] "19 genes input into functional enrichment analysis."runGprofiler("sex","Kdr-high BECs & LECs","up-regulated")## [1] "57 genes input into functional enrichment analysis."runGprofiler("sex","Kdr-high BECs & LECs","down-regulated")## [1] "34 genes input into functional enrichment analysis."# 2 genes input, no results to showrunGprofiler("sex","Doublets BECs / macrophages","down-regulated")## [1] "4 genes input into functional enrichment analysis."runGprofiler("sex","Mrc1+H2-Eb1-low macrophages","up-regulated")## [1] "46 genes input into functional enrichment analysis."runGprofiler("sex","Mrc1+H2-Eb1-low macrophages","down-regulated")## [1] "61 genes input into functional enrichment analysis."runGprofiler("sex","Mrc1+H2-Eb1-high macrophages","up-regulated")## [1] "23 genes input into functional enrichment analysis."runGprofiler("sex","Mrc1+H2-Eb1-high macrophages","down-regulated")## [1] "31 genes input into functional enrichment analysis."# 9 genes input, no results to showrunGprofiler("sex","Dendritic cells","down-regulated")## [1] "34 genes input into functional enrichment analysis."# 6 genes input, no results to showrunGprofiler("sex","Monocytes","down-regulated")## [1] "14 genes input into functional enrichment analysis."runGprofiler("sex","Neutrophils","up-regulated")## [1] "28 genes input into functional enrichment analysis."runGprofiler("sex","Neutrophils","down-regulated")## [1] "39 genes input into functional enrichment analysis."runGprofiler("sex","Mast cells","up-regulated")## [1] "18 genes input into functional enrichment analysis."runGprofiler("sex","Mast cells","down-regulated")## [1] "36 genes input into functional enrichment analysis."# 2 genes input, no results to showrunGprofiler("sex","Myeloid progenitors","down-regulated")## [1] "4 genes input into functional enrichment analysis."runGprofiler("sex","Fibroblasts","up-regulated")## [1] "67 genes input into functional enrichment analysis."runGprofiler("sex","Fibroblasts","down-regulated")## [1] "23 genes input into functional enrichment analysis."runGprofiler("sex","Schwann cells","up-regulated")## [1] "71 genes input into functional enrichment analysis."runGprofiler("sex","Schwann cells","down-regulated")## [1] "33 genes input into functional enrichment analysis."runGprofiler("sex","T cells & ILCs","up-regulated")## [1] "11 genes input into functional enrichment analysis."# 3 genes used for analysis
# only has significant results in the MIRNA source# 3 genes input, no results to show# 8 genes input, no results to show# 5 genes input, no results to showrunGprofiler("sex","Mature B cells","down-regulated")## [1] "107 genes input into functional enrichment analysis."